Squall wakes up the next day in his dormitory and his first thoughts are already of Rinoa. Normally she would have visited him during this time of day. He goes to visit Rinoa and everyone notices that he is suffering. Even Selphie mentions it on her online diary, something he won't appreciate once he finds out.
Most people don't know why he's down. To them, B-Garden just won a decisive battle and Edea is no longer a threat. Zell even tries to cheer him up, saying that Rinoa will snap out of her coma soon. Finally in the infirmary, Squall kneels by Rinoa's side, her body is cold and she doesn't move. A few moments later, Quistis pages him. They need to visit Edea at her old orphanage, which is now in ruins.
Squall, Quistis, Irvine, Zell and Selphie visit the orphanage at the Cape of Good Hope. Edea and Cid explain why they acted the way they did. Cid had to leave because he couldn't bear to lose either his children or his wife. Edea then explains how and why Ultimecia possessed her, why she allowed Ultimecia to control her and why Ellone needs to be protected. She also says Adel is still alive and that Ultimecia will be after Adel, now that her body is released.
Squall is completely distracted as the conversation goes on because the only thing on his mind right now is Rinoa. He asks Edea if she knows what is wrong with Rinoa and Cid interrupts, asking if Rinoa died. This causes Squall to react violently and punch a pile of rubble before shouting that she hasn't. Edea feels sorry for him, as she doesn't know what happened. Cid then tells Squall that he must think of how to be a leader now.
As everyone figures out what to do next, Squall's mind drifts off and he thinks of his encounters with Rinoa, how she changed him little by little and how she made him feel. She was always open with him, arguing with him, smiling at him and trying so hard to get him to change. Finally, he thinks of how she may never see how he has changed. He calls out to her in his mind and asks for another chance.
Squall dismisses everyone's protests and decides to focus on their next goal; to find and protect Ellone. They return to B-Garden to then update the SeeDs and students on the situation. Everyone visits Rinoa every once in a while and her condition remains unchanged.
Squall finds himself visiting Rinoa again in the infirmary and tries to talk to her. He puts his hand on her forehead, which is still cold. Rinoa doesn't respond to anything he says and he can't take it much longer.
While kneeling beside her, he falls asleep and has another trip to the "dream world". This time Squall is aware that it's Ellone's doing. He dreams he is Laguna, who is acting out the role of a Witch's Knight in a movie. After the dream, Ellone tries to tell Squall who his father and mother are but Squall only cares about Rinoa now. He wants to hear and see her again and believes that Ellone can help him save her.
As Squall wakes up, his first thought is wanting to hear Rinoa's voice. He tries to call for Ellone out loud but nothing happens. It is then Squall realizes that he will have to depend on others for once. He decides to ask Edea where Ellone and the White SeeD Ship is.
All of Edea's children forgive her for what happened but Xu worries that the other students may not understand or easily forgive her. According to Cid and Edea, Ellone is still travelling around the world on the ship and it's most likely near the Centra continent. Edea also gives Squall a letter, which will let the White SeeDs know that he can be trusted.
Upon finding and boarding the White SeeD Ship on a Centra coast, Squall tries to find out Ellone's location from the passengers. Apparently, the ship was caught in a cross fire between the Galbadians who were chasing them and an Esthar ship that appeared. The Esthar ship tried to offer them an escape but since they didn't trust anyone, they refused. Ellone, on the other hand, jumped and boarded the Esthar ship before they left. They don't know why, but she seemed happy.
On the deck, Squall also finds Watts and Zone. The two just barely escaped to this ship when running from Galbadians. They have made the White SeeD ship their second home and Zone even learned how to pilot it.
The first thing they ask for is Rinoa and Squall explains that she is in a comatose state. He apologizes for being unable to protect her but Zone is unforgiving. Zone takes out his anger on Squall and yells at him. He trusted Squall to take care of Rinoa and now she may have died. Watts tries to calm Zone down while Squall explains his plan to find Ellone and bring Rinoa back. Zone eventually calms down but not without making another threat towards Squall over Rinoa's safety.
Upon returning to B-Garden, Squall has everyone set course for Esthar. He then visits the infirmary. Dr. Kadowaki was just leaving her post and asks Squall to take care of things while she's gone. However, instead of staying with Rinoa, he picks her up and carries her out of the room. Squall can't take being a leader any longer and has to get away. He's unable to think straight and all he cares about is being with Rinoa now.
As soon as B-Garden reaches FH, Squall silently makes his exit with Rinoa. He is still hoping that Ellone will somehow help them. After passing through the city, he walks along the Horizon Bridge towards Esthar, just as Laguna did for Ellone long ago.
It's a long walk and the sun begins to rise again. Getting tired, Squall begins to doubt himself and his actions once more. He knows there's no guarantee Ellone can help him. Still, he realizes that he has changed. What he's doing is something Laguna would do.
Squall takes a break and sets Rinoa down, leaving her near the tracks. Facing the ocean, he wonders what everyone else is thinking of him at that moment. Instead of just thinking to himself, he finds the courage to tell Rinoa his feelings out loud, knowing that she probably can't hear him.
Squall confesses to her about his behavior, how he was introverted and unfriendly in order to keep people distanced. It's not the true side of him and only Rinoa was ever observant enough to look past it. Walking back to Rinoa, he tells her to keep it a secret. She doesn't answer though. He picks her up and resumes carrying her the rest of the way to Esthar Continent.
The sun has fully risen when Squall reaches the deserted Train Station on the Esthar Continent, only to find his own friends acting as 'Edea's escort'. They were expecting him the whole time, apparently. Zell asks if Rinoa is still asleep and calls her a princess while Quistis jokes about Rinoa possibly waking up with a kiss from the prince.
Squall is annoyed by everyone's presence until Edea explains why she must go to Esthar. Edea plans to get rid of her powers while she can with a Doctor Odine's help. The Doctor is the most knowledgeable scientist when it comes to Witches. If successful, Ultimecia will no longer be able to possess her.
Selphie and Irvine return from scouting the area to say that Esthar City must be towards the East. Selphie then takes a peek at Rinoa and whispers to Squall about how cute she looks sleeping. Squall blushes angrily and Irvine warns Selphie about making him mad.
Unable to find a city, they head out through a large frozen Salt Lake. Selphie runs ahead, missing Edea's dark comment about possibly becoming their enemy at any moment. Strangely, Squall tries to lighten the mood. He tells Edea not to mention anything bad because it might happen. It's illogical, but for once he wants to believe.
They come across a flickering wall, which shows that their surroundings were actually some sort of holographic projection to throw visitors off. Finding a passageway, they crawl up and into it as a huge high tech city before them is revealed. Now inside a building, they ride an elevator which takes them towards the inner part of the city.
Squall sets Rinoa down and thinks about the situation. He has no idea what he's doing or where he's going anymore. Still, he is going to go forward and deal with whatever comes. The elevator stops and Squall observes that with such technology, their group must have been taken there on purpose.
Before he can finish telling everyone to stay alert in case of hostility, Ellone takes him to the "dream world" once again. The dream is of why Laguna went to Esthar, he was searching for Ellone. Young Ellone was captured by a Doctor Odine and kept in a lab against her will, all because of her unique power. Odine had little regard for Ellone as a person and luckily Laguna was able to save her. Upon waking up Squall realizes that the ill-timed dream must have been a warning.
A floating car arrives at the building to pick up Squall's party and although Squall says he wants to see Ellone, Edea takes charge of the situation. They ride through the high-tech city and the man driving them says that they are going to the Presidential Palace.
When they enter the lobby, Dr. Odine greets them and Edea explains her need to be free from Ultimecia's control. Dr. Odine says that he can exorcise Ultimecia and Edea trusts him to do so. One of the Presidential Aides appears, asking for who wanted to see Ellone and Dr. Odine gives permission for Squall to go see her. However, Dr. Odine has one condition: that he be allowed to observe Rinoa's status until they are ready at the Lunar Gate. Edea tells Squall to accept the offer and he reluctantly does. Remembering Ellone's dream, Squall's protective instinct kicks in and he tells Dr. Odine that he better not do anything to Rinoa.
It seems Dr. Odine knows what is wrong with Rinoa but isn't telling anyone. Rinoa is taken to Dr. Odine's Laboratory and only afterwards she would be brought to Lunar Gate to see Ellone as well, once preparations are done.
Squall isn't allowed inside the Laboratory, but he meets a Sentry who warns him about Dr. Odine. The Sentry says that Dr. Odine doesn't care too much about people, especially when they are test subjects. He then tells Squall to make sure nothing happens to his girl. Squall isn't against the idea of people thinking they're a couple and instead of replying he thinks of killing Dr. Odine if something happens to Rinoa.
After touring Esthar, Squall's party and Edea travel by car to the Lunar Gate. When they arrive, Angelo barks and comes running inside. Squall crouches down to face Angelo and quietly assures her that he will take care of Rinoa. The Lunar Gate staff then explains what's going on. Squall, Rinoa and one other person will be travelling to visit Ellone, who is in outer space. Leaving Zell to escort Edea until her powers are suppressed, the three are loaded into capsules and then blasted into the sky.
At the base Angelo starts howling at something then runs outside. Everyone chases her to find something huge moving in the horizon, causing the ground to shake. Whatever it is, it's heading towards Esthar city. Zell's team hurries back to find out what's going on.
In Esthar, Zell's team finds Doctor Odine in high spirits at his lab. The truth is he's excited to have Rinoa and Edea as possible subjects but it turns out Lunatic Pandora is the huge thing moving across the city, causing panic and fear amongst the people. The Galbadian Army has somehow taken control of it and are steering it towards Tears' Point.
Doctor Odine investigated the Pandora in the past, when it was first excavated and put back into service. It has been left alone for nearly two decades until now and since the Galbadian Army is using it for no good, Zell's team needs to find a way to stop it. Odine gives them some advice on boarding the Pandora but doesn't tell the full story behind what Lunatic Pandora is. It becomes apparent that Galbadia is not behind everything.
Zell's party finally boards the Pandora, which is loaded with Galbadian Officers. Before they can make their way deep inside and find out what's going on, they get forcibly teleported off of it. They watch as Lunatic Pandora positions itself at Tears' Point and the statues come to life. Having been a Witch, Edea senses that this is the start of a Lunar Cry. The party decides to fall back, as this is far beyond their control.
Meanwhile in outer space., Squall and Rinoa have arrived at the Lunar Base. One of the Medical Staff immediately begins checking Rinoa's status and asking if she's dead. This angers Squall and he tells everyone not to touch Rinoa as he carries her. Piet greets them and leads Squall to the med lab, where they will leave Rinoa. Before leaving, Squall reminds the Medical Staff not to touch Rinoa again. Seeing Squall's over protectiveness, the staff member says that Squall must be her Knight.
Piet leads Squall to the control room as the observe a rare phenomenon. Normally they would monitor Adel, the Witch who is sealed, but at the moment a Lunar Cry is beginning. Whenever irregularities (natural and unnatural) between the Moon and Earth's gravity occurs, it pulls monsters from the Moon down towards their planet. The last one, which occurred 100 years ago wiped out the main city on the Centra continent and created a huge crater.
After watching the strange thing occurring on the moon, Squall finally gets his chance to meet Ellone. On his way to her room, he sees that the President of Esthar is personally conducting an inspection on Adel's Tomb in outer space. Barely paying any attention to the spectacle, he enters Ellone's room and breathes a sigh of relief as they are finally reunited.
Ellone explains her realization and says that she can't change the past with her powers. Squall says he understood why she made him experience the memories and what she was trying to do. However, she was trying to teach Squall what she had learnt. From learning things about the past, they would see things differently in the present.
Squall immediately gets to his point, saying he needs Ellone's help in order to see Rinoa's past. He wants to find out what happened to her and possibly warn her. Ellone apologetically says she can't do it because she simply doesn't know Rinoa. Squall then tells Ellone that Rinoa is with him and he takes Ellone to her.
Meanwhile, Rinoa's capsule bed eerily opens by itself and she exits the lab. She knocks away anyone who tries to stop her while after-images of her body trail behind. The alarms go off and a staff member announces for all units to report to the med lab. Feeling something is wrong with Rinoa, Squall tells Ellone to wait in the control room while he goes to check. He finds the ghostly Rinoa gliding through the halls and tries to get through to her but can't, as he is knocked away from her each time.
Rinoa floats toward the control room and begins deactivating the Seals on Adel's Tomb. No one is able to stop her because of the magic shielding her. At the same time, monsters are now heavily flocking towards one spot on the Moon's surface and the Lunar Cry is beginning. Squall does everything he can to try and stop Rinoa but he's always a step behind. Before he knows it, Rinoa is in outer space. and getting in position to unlock the last Seal on Adel's Tomb.
To one of the people at the Base it seemed like everything happening was actually planned out. The Lunar Base and Tomb are positioned just between the Moon and Earth. Rinoa was taken to the Base and now for some reason she's trying to revive Adel, whose Tomb would surely fall down to earth along with the Lunar Cry. Only Squall knows whose plan this was: Ultimecia's.
Despite the chaos of the Lunar Base being evacuated, Squall tries to follow Rinoa into outer space. Adel is revived and a smile creeps upon her face just as the Tomb is swallowed up by the Lunar Cry, and falls towards the Earth. Luckily, Rinoa luckily doesn't fall down with Adel but her spacesuit has limited oxygen and time for her begins to run out.